A special over sample of charter schools, conducted as part of the 2003 fourth-grade NAEP assessments, permitted a comparison of academic achievement for students enrolled in charter schools to that for students enrolled in traditional public schools. The school sample comprised 150 charter schools and 6,764 traditional public schools. The report uses hierarchical linear models (HLMs) to examine differences between the two types of schools when multiple student and/or school characteristics are taken into account. After adjusting for student demographic characteristics, charter school mean scores in reading and mathematics were lower, on average, than those for traditional public schools. The size of these differences was smaller in reading than in mathematics. Results from the second analysis showed that in reading and mathematics, average performance differences between traditional public schools and charter schools affiliated with a public school district were not statistically significant, while charter schools not affiliated with a public school district scored significantly lower on average than traditional public schools.